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biopet.biopet
Commit 39070750 authored by Sander Bollen's avatar Sander Bollen
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Merge branch 'fix-BIOPET-473' into 'develop' 

Fixing BIOPET-473



See merge request !482
parents af90c666 a4292fbc
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Showing with 24 additions and 3 deletions
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 39070750
......@@ -46,6 +46,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
def indexPage = {
val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
val insertsizeExecuted = summary.getSampleValues("bammetrics", "stats", "CollectInsertSizeMetrics", "metrics").values.exists(_ != Some(None))
......@@ -56,9 +57,15 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
(if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
(if (krakenExecuted) List("Dustbin analysis - Kraken" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ++ (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report")
)), Map())), List(
"Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report")
)), Map("summaryModuleTag" -> "gearscentrifuge")))
else Nil) ++
List("Reference" -> ReportPage(List(), List(
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
......@@ -109,13 +116,20 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
.exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None)) ++
(if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report")
)), Map())), List(
"Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report")
)), Map("summaryModuleTag" -> "gearscentrifuge")))
else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
"Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ++
......@@ -133,12 +147,19 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil) :::
(if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
(if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_report")
)), Map())), List(
"Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report")
)), Map("summaryModuleTag" -> "gearscentrifuge")))
else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
"Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil),
......
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